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Items: 20


SynFind: compiling syntenic regions across any set of genomes on demand.

Tang H, Bomhoff MD, Briones E, Zhang L, Schnable JC, Lyons E.

Genome Biol Evol. 2015 Nov 11. pii: evv219. [Epub ahead of print]


Impacts of Whole-Genome Triplication on MIRNA Evolution in Brassica rapa.

Sun C, Wu J, Liang J, Schnable JC, Yang W, Cheng F, Wang X.

Genome Biol Evol. 2015 Nov 1;7(11):3085-96. doi: 10.1093/gbe/evv206.


Phylogeny and photosynthesis of the grass tribe Paniceae.

Washburn JD, Schnable JC, Davidse G, Pires JC.

Am J Bot. 2015 Sep;102(9):1493-505. doi: 10.3732/ajb.1500222. Epub 2015 Sep 15.


Microsatellite Variations of Elite Setaria Varieties Released during Last Six Decades in China.

Jia G, Liu X, Schnable JC, Niu Z, Wang C, Li Y, Wang S, Wang S, Liu J, Guo E, Zhi H, Diao X.

PLoS One. 2015 May 1;10(5):e0125688. doi: 10.1371/journal.pone.0125688. eCollection 2015.


ALLMAPS: robust scaffold ordering based on multiple maps.

Tang H, Zhang X, Miao C, Zhang J, Ming R, Schnable JC, Schnable PS, Lyons E, Lu J.

Genome Biol. 2015 Jan 13;16:3. doi: 10.1186/s13059-014-0573-1.


Genome evolution in maize: from genomes back to genes.

Schnable JC.

Annu Rev Plant Biol. 2015;66:329-43. doi: 10.1146/annurev-arplant-043014-115604. Epub 2014 Dec 1.


Nonsyntenic genes drive highly dynamic complementation of gene expression in maize hybrids.

Paschold A, Larson NB, Marcon C, Schnable JC, Yeh CT, Lanz C, Nettleton D, Piepho HP, Schnable PS, Hochholdinger F.

Plant Cell. 2014 Oct;26(10):3939-48. doi: 10.1105/tpc.114.130948. Epub 2014 Oct 14.


Two evolutionarily distinct classes of paleopolyploidy.

Garsmeur O, Schnable JC, Almeida A, Jourda C, D'Hont A, Freeling M.

Mol Biol Evol. 2014 Feb;31(2):448-54. doi: 10.1093/molbev/mst230. Epub 2013 Dec 1.


Automated conserved non-coding sequence (CNS) discovery reveals differences in gene content and promoter evolution among grasses.

Turco G, Schnable JC, Pedersen B, Freeling M.

Front Plant Sci. 2013 Jul 2;4:170. doi: 10.3389/fpls.2013.00170. eCollection 2013.


Escape from preferential retention following repeated whole genome duplications in plants.

Schnable JC, Wang X, Pires JC, Freeling M.

Front Plant Sci. 2012 May 15;3:94. doi: 10.3389/fpls.2012.00094. eCollection 2012.


Fractionation mutagenesis and similar consequences of mechanisms removing dispensable or less-expressed DNA in plants.

Freeling M, Woodhouse MR, Subramaniam S, Turco G, Lisch D, Schnable JC.

Curr Opin Plant Biol. 2012 Apr;15(2):131-9. doi: 10.1016/j.pbi.2012.01.015. Epub 2012 Feb 14. Review.


Altered patterns of fractionation and exon deletions in Brassica rapa support a two-step model of paleohexaploidy.

Tang H, Woodhouse MR, Cheng F, Schnable JC, Pedersen BS, Conant G, Wang X, Freeling M, Pires JC.

Genetics. 2012 Apr;190(4):1563-74. doi: 10.1534/genetics.111.137349. Epub 2012 Feb 2.


Genome-wide analysis of syntenic gene deletion in the grasses.

Schnable JC, Freeling M, Lyons E.

Genome Biol Evol. 2012;4(3):265-77. doi: 10.1093/gbe/evs009. Epub 2012 Jan 23.


Heritable epigenetic variation among maize inbreds.

Eichten SR, Swanson-Wagner RA, Schnable JC, Waters AJ, Hermanson PJ, Liu S, Yeh CT, Jia Y, Gendler K, Freeling M, Schnable PS, Vaughn MW, Springer NM.

PLoS Genet. 2011 Nov;7(11):e1002372. doi: 10.1371/journal.pgen.1002372. Epub 2011 Nov 17.


High-resolution mapping of open chromatin in the rice genome.

Zhang W, Wu Y, Schnable JC, Zeng Z, Freeling M, Crawford GE, Jiang J.

Genome Res. 2012 Jan;22(1):151-62. doi: 10.1101/gr.131342.111. Epub 2011 Nov 22.


Screening synteny blocks in pairwise genome comparisons through integer programming.

Tang H, Lyons E, Pedersen B, Schnable JC, Paterson AH, Freeling M.

BMC Bioinformatics. 2011 Apr 18;12:102. doi: 10.1186/1471-2105-12-102.


Genes identified by visible mutant phenotypes show increased bias toward one of two subgenomes of maize.

Schnable JC, Freeling M.

PLoS One. 2011 Mar 10;6(3):e17855. doi: 10.1371/journal.pone.0017855.


Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss.

Schnable JC, Springer NM, Freeling M.

Proc Natl Acad Sci U S A. 2011 Mar 8;108(10):4069-74. doi: 10.1073/pnas.1101368108. Epub 2011 Feb 22.


Dose-sensitivity, conserved non-coding sequences, and duplicate gene retention through multiple tetraploidies in the grasses.

Schnable JC, Pedersen BS, Subramaniam S, Freeling M.

Front Plant Sci. 2011 Mar 10;2:2. doi: 10.3389/fpls.2011.00002. eCollection 2011.


Following tetraploidy in maize, a short deletion mechanism removed genes preferentially from one of the two homologs.

Woodhouse MR, Schnable JC, Pedersen BS, Lyons E, Lisch D, Subramaniam S, Freeling M.

PLoS Biol. 2010 Jun 29;8(6):e1000409. doi: 10.1371/journal.pbio.1000409.

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